data_5HVM
#
_model_server_result.job_id            N-Bim8Dsf0qh6L19-4mRJQ 
_model_server_result.datetime_utc      '2024-11-08 19:38:36' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          5hvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":601}' 
#
_entry.id    5HVM 
#
_exptl.entry_id    5HVM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5HVM 
_cell.length_a            83.915 
_cell.length_b            101.153 
_cell.length_c            146.992 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5HVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA tetrameric 4 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1 
A,B,C,D,E,F,G,H 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
N1 C2 UDP sing 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     5HVM 
_atom_sites.fract_transf_matrix[1][1]    0.011917 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009886 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.006803 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 2 UDP A 1 601 601 UDP UDP . 
D 3 VDM A 1 602 602 VDM VDM . 
E 2 UDP B 1 601 601 UDP UDP . 
F 3 VDM B 1 602 602 VDM VDM . 
G 4 HOH A 1 701 5 HOH HOH . 
G 4 HOH A 2 702 3 HOH HOH . 
G 4 HOH A 3 703 2 HOH HOH . 
G 4 HOH A 4 704 6 HOH HOH . 
G 4 HOH A 5 705 1 HOH HOH . 
G 4 HOH A 6 706 7 HOH HOH . 
H 4 HOH B 1 701 8 HOH HOH . 
H 4 HOH B 2 702 4 HOH HOH . 
H 4 HOH B 3 703 9 HOH HOH . 
H 4 HOH B 4 704 10 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N1 UDP . . . E 2 11.933 14.129 23.637 1 50.64 ? N1 UDP 601 B 1 
HETATM 2 C C2 UDP . . . E 2 10.877 13.357 24.278 1 60.99 ? C2 UDP 601 B 1 
HETATM 3 N N3 UDP . . . E 2 10.979 11.915 24.428 1 57.01 ? N3 UDP 601 B 1 
HETATM 4 C C4 UDP . . . E 2 12.13 11.258 23.942 1 56.76 ? C4 UDP 601 B 1 
HETATM 5 C C5 UDP . . . E 2 13.196 12.032 23.292 1 49.27 ? C5 UDP 601 B 1 
HETATM 6 C C6 UDP . . . E 2 13.08 13.483 23.141 1 44.12 ? C6 UDP 601 B 1 
HETATM 7 O O2 UDP . . . E 2 9.894 13.93 24.689 1 74.78 ? O2 UDP 601 B 1 
HETATM 8 O O4 UDP . . . E 2 12.226 10.048 24.064 1 64.9 ? O4 UDP 601 B 1 
HETATM 9 C C1' UDP . . . E 2 11.714 15.492 23.549 1 60.8 ? C1' UDP 601 B 1 
HETATM 10 C C2' UDP . . . E 2 12.682 16.238 23.037 1 64.52 ? C2' UDP 601 B 1 
HETATM 11 O O2' UDP . . . E 2 13.762 16.545 23.989 1 57.2 ? O2' UDP 601 B 1 
HETATM 12 C C3' UDP . . . E 2 11.87 17.515 22.71 1 68.84 ? C3' UDP 601 B 1 
HETATM 13 C C4' UDP . . . E 2 10.513 16.92 22.156 1 57.07 ? C4' UDP 601 B 1 
HETATM 14 O O4' UDP . . . E 2 10.501 15.673 22.487 1 59.85 ? O4' UDP 601 B 1 
HETATM 15 O O3' UDP . . . E 2 11.619 18.261 23.785 1 53.55 ? O3' UDP 601 B 1 
HETATM 16 C C5' UDP . . . E 2 10.492 17.077 20.66 1 44.28 ? C5' UDP 601 B 1 
HETATM 17 O O5' UDP . . . E 2 10.149 18.421 20.516 1 46.98 ? O5' UDP 601 B 1 
HETATM 18 P PA UDP . . . E 2 10.075 19.131 19.123 1 50.21 ? PA UDP 601 B 1 
HETATM 19 O O1A UDP . . . E 2 11.389 19.014 18.392 1 55.89 ? O1A UDP 601 B 1 
HETATM 20 O O2A UDP . . . E 2 9.724 20.575 19.384 1 53.07 ? O2A UDP 601 B 1 
HETATM 21 O O3A UDP . . . E 2 8.994 18.466 18.19 1 56.67 ? O3A UDP 601 B 1 
HETATM 22 P PB UDP . . . E 2 7.581 17.92 18.598 1 51.11 ? PB UDP 601 B 1 
HETATM 23 O O1B UDP . . . E 2 6.73 17.953 17.356 1 66.15 ? O1B UDP 601 B 1 
HETATM 24 O O2B UDP . . . E 2 6.985 18.784 19.669 1 63.5 ? O2B UDP 601 B 1 
HETATM 25 O O3B UDP . . . E 2 7.731 16.497 19.063 1 58.58 ? O3B UDP 601 B 1 
HETATM 26 H HN3 UDP . . . E 2 10.312 11.443 24.833 1 68.41 ? HN3 UDP 601 B 1 
HETATM 27 H H5 UDP . . . E 2 13.989 11.574 22.956 1 59.12 ? H5 UDP 601 B 1 
HETATM 28 H H6 UDP . . . E 2 13.792 13.995 22.712 1 52.94 ? H6 UDP 601 B 1 
HETATM 29 H H1' UDP . . . E 2 11.448 15.844 24.423 1 72.96 ? H1' UDP 601 B 1 
HETATM 30 H H2' UDP . . . E 2 13.038 15.834 22.221 1 77.42 ? H2' UDP 601 B 1 
HETATM 31 H HO2' UDP . . . E 2 13.721 17.404 24.216 1 68.64 ? HO2' UDP 601 B 1 
HETATM 32 H H3' UDP . . . E 2 12.321 18.042 22.02 1 82.61 ? H3' UDP 601 B 1 
HETATM 33 H H4' UDP . . . E 2 9.751 17.384 22.556 1 68.48 ? H4' UDP 601 B 1 
HETATM 34 H HO3' UDP . . . E 2 12.312 18.799 23.942 1 64.26 ? HO3' UDP 601 B 1 
HETATM 35 H "H5'1" UDP . . . E 2 11.378 16.9 20.281 1 53.14 ? "H5'1" UDP 601 B 1 
HETATM 36 H "H5'2" UDP . . . E 2 9.812 16.497 20.261 1 53.14 ? "H5'2" UDP 601 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           36 
#